Filipe Jorge Coelho posted a comment on discussion Help

I need to know the bootstrap method used by defaul in AMOS. Can somebody help? Thanks ...

renekat posted a comment on ticket #28

Hello, I'm having this issue too.

Javier created ticket #4

stopping in step 41

Francesco Cicconardi posted a comment on ticket #29

Hi, This is the new log. ESC[0;35m###### Wed Apr 22 05:43:48 BST 2020: Running layoutESC[0m INPUT reads lis mates PLACEMENT CONFLICT ASSEMBLY OUTPUT ESC[0;35m###### Sun Apr 26 17:18:38 BST 2020: Running consensusESC[0m Entering 'Amos_supercontigs.bnk' Found CTG bank unlocking 'r 432968 tk19812' Found FRG bank Found LAY bank Found LIB bank Found RED bank Found SCF bank Found UNV bank IFOs found: 7 File locks: 0 Bank locks: 1 Starting on Sun Apr 26 17:18:38 2020 Read bank is Amos_supercontigs.bnk Alignment...

Francesco Cicconardi posted a comment on ticket #29

I'm suspecting it's a memory issue. Is there any chance I can split the delta file to run part of that and reconnect them after? Cheers F

Francesco Cicconardi posted a comment on ticket #29

Now I don't have it anymore, but the log file was just listing the different stages of the job like: INPUT reads lis ... till the end without returning any expicit error. F

ddsommer posted a comment on ticket #29

Yes that is correct it is failing because of the missing CTG files. Is there a amos log file with logging from the casm-layout step? On Sat, Apr 25, 2020 at 12:34 PM Francesco Cicconardi francicco@users.sourceforge.net wrote: Hi, I think consensus fails because layout didn't generate the file. layout also finishes without error messages Thanks a lot F [bugs:#29] https://sourceforge.net/p/amos/bugs/29/ casm-layout ERROR* Status: open Group: v1.x.x Created: Wed Apr 15, 2020 02:37 PM UTC by Francesco...

Francesco Cicconardi posted a comment on ticket #29

Hi, I think consensus fails because layout didn't generate the file. layout also finishes without error messages Thanks a lot F

ddsommer posted a comment on ticket #29

How are you running "concensus" if the casm-layout program had already failed to produce the CTG bank files? What was the error or log from casm-layout? On Wed, Apr 15, 2020 at 10:37 AM Francesco Cicconardi francicco@users.sourceforge.net wrote: Unfortunately casm-layout: casm-layout -t 1000 -U ${supercontigs}.layout -C ${supercontigs}.conflict -b ${supercontigs}.bnk ${supercontigs}.delta fails to generate the some files, specifically CTG.0.map, CTG.0.0.fix and CTG.0.0.var I get the following error...

Francesco Cicconardi created ticket #29

casm-layout ERROR

von_klatka posted a comment on ticket #28

I have exactly the same problem...

Sergey Potapov posted a comment on discussion Help

Hello, Lisa! I have install problem to. May be this help you https://vcru.wisc.edu/simonlab/bioinformatics/programs/install/amos.htm

Lisa Jones posted a comment on discussion Help

I am not sure what to do anymore can anyone help me. it looks like i am having problems with utility_AMOS Thanks Attached it the errors.

potant posted a comment on ticket #28

by using CXXFLAGS="$CXXFLAGS -Wno-narrowing" in configure, it solves the problem. But then, when i press make, it gives these errors: .... make[3]: Entering directory '/home/potant/Downloads/amos-3.1.0/src/Align' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -Wno-narrowing -Wcpp -MT genome-complexity-fast.o -MD -MP -MF .deps/genome-complexity-fast.Tpo -c -o genome-complexity-fast.o genome-complexity-fast.cc...

Martin Mokrejs created ticket #28

x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS -I../.. -O2 -pipe -O2 -pipe -march=native -ftree-vectorize -Wno-cpp -c -o libAMOS_a-utility_AMOS.o `test -f 'utility_AMOS.cc' || echo '/apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/'`utility_AMOS.cc In file included from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.hh:13, from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:10: /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/inttypes_AMOS.hh: In function 'std::__cxx11::string AMOS::Decode(AMOS::NCode_t)': /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/inttypes_AMOS.hh:78:25: warning: narrowing conversion of '(ncode & 127)' from 'AMOS::NCode_t' {aka 'unsigned int'} to 'char' inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/inttypes_AMOS.hh:78:55: warning: narrowing conversion of '((ncode >> 8) & 127)' from 'AMOS::NCode_t' {aka 'unsigned int'} to 'char' inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/inttypes_AMOS.hh:79:35: warning: narrowing conversion of '(((ncode >> 8) >> 8) & 127)' from 'AMOS::NCode_t' {aka 'unsigned int'} to 'char' inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ In file included from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.hh:13, from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/Message_AMOS.hh:14, from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/Universal_AMOS.hh:13, from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/Link_AMOS.hh:13, from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/Edge_AMOS.hh:13, from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/ContigEdge_AMOS.hh:13, from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/universals_AMOS.hh:13, from /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/universals_AMOS.cc:10: /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/inttypes_AMOS.hh: In function 'std::__cxx11::string AMOS::Decode(AMOS::NCode_t)': /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/inttypes_AMOS.hh:78:25: warning: narrowing conversion of '(ncode & 127)' from 'AMOS::NCode_t' {aka 'unsigned int'} to 'char' inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/inttypes_AMOS.hh:78:55: warning: narrowing conversion of '((ncode >> 8) & 127)' from 'AMOS::NCode_t' {aka 'unsigned int'} to 'char' inside { } [-Wnarrowing] char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX, ^ /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/inttypes_AMOS.hh:79:35: warning: narrowing conversion of '(((ncode >> 8) >> 8) & 127)' from 'AMOS::NCode_t' {aka 'unsigned int'} to 'char' inside { } [-Wnarrowing] ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'}; ^ /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc: At global scope: /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '128' from 'int' to 'char' inside { } [-Wnarrowing] }; ^ /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '129' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '130' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '131' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '132' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '133' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '134' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '135' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '136' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '137' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '138' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '139' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '140' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '141' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '142' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '143' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '144' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '145' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '146' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '147' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '148' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '149' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '150' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '151' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '152' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '153' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '154' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '155' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '156' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '157' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '158' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '159' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '160' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '161' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '162' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '163' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '164' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '165' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '166' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '167' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '168' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '169' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '170' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '171' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '172' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '173' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '174' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '175' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '176' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '177' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '178' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '179' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '180' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '181' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '182' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '183' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '184' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '185' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '186' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '187' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '188' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '189' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '190' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '191' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '192' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '193' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '194' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '195' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '196' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '197' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '198' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '199' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '200' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '201' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '202' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '203' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '204' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '205' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '206' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '207' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '208' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '209' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '210' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '211' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '212' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '213' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '214' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '215' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '216' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '217' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '218' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '219' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '220' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '221' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '222' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '223' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '224' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '225' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '226' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '227' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '228' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '229' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '230' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '231' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '232' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '233' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '234' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '235' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '236' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '237' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '238' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '239' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '240' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '241' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '242' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '243' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '244' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '245' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '246' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '247' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '248' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '249' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '250' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '251' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '252' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '253' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '254' from 'int' to 'char' inside { } [-Wnarrowing] /apps/gentoo/var/tmp/portage/sci-biology/amos-9999/work/amos-9999/src/AMOS/utility_AMOS.cc:35:3: error: narrowing conversion of '255' from 'int' to 'char' inside { } [-Wnarrowing] make[3]: *** [Makefile:1059: libAMOS_a-utility_AMOS.o] Error 1

Martin Mokrejs created ticket #27

src/Align/genome-complexity-fast.cc:602:26: error: qualified-id in declaration before 'm'

David posted a comment on discussion Help

Hi, I am running a amos pipleline that produced the following error: hash-overlap -B -o 35 -x .020 -v 0 ./all.bnk exited with status: 1 What does exited with status: 1 mean?

Elliot Maltz posted a comment on discussion Help

I am creating a measurement model with 12 latent variables and want to create correlations...

Jeff modified a comment on ticket #20

Thanks for the patch, it updated the path vars in minimus2! If anyone could benefit...

Jeff modified a comment on ticket #20

Thanks for the patch, it updated the path vars in minimus2! However, there is still...

Jeff modified a comment on ticket #20

Thanks for the patch, it updated the path vars in minimus2! However, there is still...

Jeff modified a comment on ticket #20

Thanks for the patch, it updated the path vars in minimus2! However, there is still...

Jeff modified a comment on ticket #20

Thanks for the patch, it updated the path vars in minimus2! However, there is still...

Jeff posted a comment on ticket #20

Thanks for the patch, it worked! If anyone could benefit from the steps: first installed...

Simon modified a comment on ticket #25

Try: https://github.com/nathanhaigh/amos

Simon posted a comment on ticket #25

See: https://github.com/nathanhaigh/amos

Brian Walenz posted a comment on ticket #25

Impacts: FreeBSD-9.1 with gcc 4.8 OS X 10.9.5 with gcc 4.9 from MacPorts

Michael Schatz committed [c9e6d8]

add nchart

Michael Schatz committed [ad2386]

add find-redundant.pl

Michael Schatz committed [9bd658]

Merge branch 'master' of ssh://git.code.sf.net/...

AMOS released /OldFiles/Figaro-1.0.tar.gz

AMOS released /OldFiles/AMOS_2_0_1.tgz

AMOS released /OldFiles/amos-2.0.6.tar.gz

Milo modified a comment on discussion Help

Hello, I am using the following protocol to Merge a multikmer assembly using CDHit...

Milo posted a comment on discussion Help

Hello, I am using the following protocol to Merge a multikmer assembly using CDHit...

Milo created ticket #3

Minimus2 stuck at step 20

Adam Phillippy posted a comment on discussion Open Discussion

ERROR! The markdown supplied could not be parsed correctly. Did you forget to surround...

ddsommer posted a comment on discussion Open Discussion

The wiki is back up and running at http://amos.sourceforge.net/wiki/index.php/AMOS...

ddsommer modified a wiki page

Home

Alex Weisberg posted a comment on discussion Help

I am having some trouble running minimus2 on centos 7, I have my .afg file containing...

yo bargsten posted a comment on ticket #20

here is a patch for the DELTAFILTER and SHOWCOORDS variables. It seems that the variables...

Adam Phillippy posted a comment on discussion Open Discussion

ERROR! The markdown supplied could not be parsed correctly. Did you forget to surround...

Nathan Jones posted a comment on discussion Open Discussion

Where did the detailed wiki of all the features, components and examples of the myriad...

Adam Phillippy posted a comment on discussion Open Discussion

ERROR! The markdown supplied could not be parsed correctly. Did you forget to surround...

Florian posted a comment on discussion Open Discussion

Hello everyone, first of all thanks for this great program to the developers and...

Sergey Koren committed [7ec77c]

Bug fix for segfault while calculating alignments

Sergey Koren committed [60d4e5]

Merge branch 'master' of ssh://git.code.sf.net/...

Connor Skennerton created ticket #2

More robust fasta parsing in samtoarg.pl

Connor Skennerton created ticket #26

Error in Message parsing code when final qlt field char is '.'